Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.
A large statue of Charles Darwin was installed in the main foyer of the London's Natural History Museum in 1885—just a few years after Darwin's death. It was removed in 1927 and replaced by a statue of Richard Owen who was no fan of Darwin.
The museum came to its senses in 2009 and put the statue back in it's original position. (It had been in the cafeteria in the basement.) Read the story at: Moving Darwin.
Owen was the man who founded the museum and he was also known for his support of structuralism—the idea that basic body plans cannot be easily explained by evolution. Structuralism is the new buzzword among Intelligent Design Creationists. They don't understand the concept but they're certain it refutes evolution and supports goddidit.
Watch Paul Nelson combine his lack of knowledge of evolution and evolutionary theory with misinformation (i.e. lies) and a little bit of false developmental biology then stir the pot with a large dose of god-of-the-gaps to produce a smooth argument that refutes evolution.
There's lots of other stuff going on in this talk. I was especially amused by the discussion of methodological naturalism at the end. Paul Nelson argues that science is blind to all the evidence of a creator because the "rule" of science is that it can't even consider that evidence.
I'll say one thing about this talk: it's very clever. It would take a book to show that Paul Nelson is wrong about everything and the explanations would be far too complicated for the average creationist. For them, it's easier to believe that Paul Nelson is telling them the truth and evolutionary biologists are too stupid to understand their own discipline.
Otangelo Grasso has posted a transcript of the talk. Thank-you Otangelo.
The draft sequences of the human genome were published fifteen years ago. The International Human Genome Project (IGHP) published its draft sequence in Nature on Feb. 15, 2001 (Lander et al., 2001) and Celera Genomics published its draft sequence in Science on Feb. 16, 2001 (Venter et al., 2001).1
For me the timing was perfect since I was scheduled to give a Journal Club talk on March 16th and you could hardly ask for a better topic.
Antonin Gregory Scalia (March 11, 1936 – February 13, 2016), justice of the Supreme Court of the United States, died a few days ago. This creates a crisis in American politics because they have a strange set of Constitutional requirements guaranteed to maximize the probability of crises every time they need a new Supreme Court justice.
Scalia's death reminded me of the dissenting opinion in EDWARDS V. AGUILLARD (June 19, 1987). This was the case that invalidated Louisiana's "Balanced Treatment for Creation-Science and Evolution-Science Act." Stephen Jay Gould was puzzled by the dissenting opinion so he wrote a wonderful essay to explain Justice Scalia's Misunderstanding.
It's worth reading the entire essay but here's the conclusion,
Following this theme, Scalia presents his most confused statement in the written dissent:
Creation science, its proponents insist, no more must explain whence life came than evolution must explain whence came the inanimate materials from which it says life evolved. But even if that were not so, to posit a past creator is not to posit the eternal and personal God who is the object of religious veneration.
True indeed; one might be a creationist in some vernacular sense by maintaining a highly abstract and impersonal view of the creator. But Aristotle's unmoved mover is no more part of science than the Lord of Genesis. Science does not deal with questions of ultimate origins. We would object just as strongly if the Aristotelophiles of Delaware forced a law through the state legislature requiring that creation of each species ex nihilo by an unmoved mover be presented every time evolution is discussed in class. The difference is only historical circumstance, not the logic of argument The unmoved mover doesn't pack much political punch; fundamentalism ranks among our most potent irrationalisms.
Consider also, indeed especially, Scalia's false concept of science. He equates creation and evolution because creationists can't explain life's beginning, while evolutionists can't resolve the ultimate origin of the inorganic components that later aggregated to life. But this inability is the very heart of creationist logic and the central reason why their doctrine is not science, while science's inability to specify the ultimate origin of matter is irrelevant because we are not trying to do any such thing. We know that we can't, and we do not even consider such a question as part of science.
We understand Hutton's wisdom. We do not search for unattainable ultimates.
We define evolution, using Darwin's phrase, as "descent with modification" from prior living things. Our documentation of life's evolutionary tree records one of science's greatest triumphs, a profoundly liberating discovery on the oldest maxim that truth can make us free. We have made this discovery by recognizing what can be answered and what must be left alone. If Justice Scalia heeded our definitions and our practices, he would understand why creationism cannot qualify as science. He would also, by the way, sense the excitement of evolution and its evidence; no person of substance could be unmoved by something so interesting. Only Aristotle's creator may be so impassive.
Who was Saint Valentine? Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer1 sometime around 1380.
It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?
Readers of this blog will know that I'm a fan of Evolution by Accident. I don't think that the history of life can be explained in strict Darwinian terms (i.e. natural selection) and I think that modern evolutionary theory includes Neutral Theory and a major role for random genetic drift.
This is the view of many modern evolutionary biologists. Their work and views have been reported frequently on Sandwalk over the past ten years but you can find it in all the evolutionary biology textbooks. I'm just the messenger here. It's evolutionary biologists who have made the case for non-adaptive evolution beginning long before The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.
This is another post about the stupidity of Intelligent Design Creationists. Stop reading if you don't need any more convincing.
Today is Darwin Day. It's the anniversary of the birth of Charles Darwin (Feb. 12, 1809 - April 19, 1882).
This is not a happy day for the Discovery Institute so they've put up a series of posts on Evolution News & Views (sic) to discredit Darwin and "Darwinism."
To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive—that is, helpful to the organism in flourishing in its environment—and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.
That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.
Strictly speaking, that's a reasonable explanation of Darwinism as most evolutionary biologists understand it. But here's the problem. There aren't very many evolutionary biologists who are strict Darwinists these days even though there are many who tilt strongly in that direction.
Intelligent Design Creationists are promoting a structuralist view of evolution [What is structuralism?]. The idea is that the history of life as we know it was largely preordained by the initial laws of physics and chemistry. According to this view, once life got under way it was inevitable that it would eventually evolve the way it did resulting in humans or something that closely resembles humans.
Structuralism is based on the idea of intrinsic forms that severely limit evolutionary pathways. These forms are constrained, and defined, by the physics of matter and energy. Some creationists like this idea because they believe that god created the universe and fine-tuned it for life. According to their faith, once the original laws of physics and chemistry were set up it was just a matter of time before humans evolved. These creationists can make their belief in a creator god compatible with evolution as they see it.
(Let's not forget that there are many structuralists who are legitimate scientists and some of them are atheists. Structuralism is not a creationist invention.)
The conflict between structuralists and others is brought into focus by Stephen Jay Gould writing in Wonderful Life.
The blog "Conceptual Revolutions in Science" only publishes "evidence-based, paradigm-shifting scientific news" according to their home page.
The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.
Some of you are aware of recent attacks on Richard Dawkins. This video by Brian Dalton (Mr. Deity)1 is directed at certain people who have led the attacks. Some of them are my friends but I'm having second thoughts. They should pay close attention.
I disagree with several scientific ideas that Richard Dawkins has promoted and we have discussed these disagreements in person and on the internet. I've always found him to be polite and respectful.
Michael Denton and the Discovery Institute are promoting his new book, Evolution: Still a Theory in Crisis. I haven't yet read the book. I ordered from Amazon.ca and I won't get it until March.
The essence of the fine-tuning argument is that the basic laws of physics and chemistry are so precise that even slight changes would result in a universe where life is impossible. The focus is usually on the fundamental constants such as the speed of light and the charge on an electron. I don't know enough about physics to evaluate the argument that these are fine-tuned so I have to rely on physicists to inform me.
All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.
Matthew Cobb wasn't happy with the way Denis Alexander reviewed Jerry Coyne's book. Recall that Denis Alexander is a biochemist at Cambridge University (UK) and we had a little debate a week or so ago [Is there a conflict between science and religion?]. His position is that there's no conflict between science and religion because a person who believes in god can always make their views conform to the discoveries of science. I didn't accept his premise—that gods exist—so we had a discussion about whether there's any evidence to support his belief in god.
If you believe in such a being then that conflicts with science as a way of knowing because you are believing in something without reliable evidence to support your belief. Scientists shouldn't do that and neither should any others who practice the scientific way of knowing. Denis Alexander thinks there are other, equally valid, ways of knowing but he wasn't able to offer any evidence that those other ways produce true knowledge.
Matthew Cob wrote a letter to the editor in which he asked, "I wonder if Dr Alexander, or indeed any reader, could provide an example of knowledge gained through theology, and above all tell us how they know that knowledge is true?" [see Matthew Cobb battles with the faithful over my book].
Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.
I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.
Try the quiz yourself before reading any further. There are spoilers below!
The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.
You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.
You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.
If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.
If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.
You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?
I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.
Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.
It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).
Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.
Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.
I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").
It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.
Currently there are two distinct views on the origin of life. The majority of scientists think that life arose in a prebiotic soup of complex organic molecules. Most of them think this "warm little pond" was the ocean (!) and most of them have bought into the stories about asteroids and comets delivering complex organic molecules to create a soup of amino acids and sugars. Presumably, all the earliest forms of life had to do was to join together the amino acids to make proteins and hook up the nucleotides to make RNA. The energy for these reactions was derived from breaking down all the glucose in the sweet ocean.
James McGrath is a professor of religion at Butler University in Indianapolis, Indiana, USA.
He is one of those "sophisticated theologians" who dismiss modern atheists because we haven't spent years studying theology and because we haven't experienced the true existential angst of Jean-Paul Sartre. As a group, they hold to the position that the "New Atheists" are amateurs in the study of religion and their arguments can be easily dismissed.
Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."
There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.
Confirmation bias is one of the major logical fallacies. When philosopher Chris DiCarlo and I were teaching a course on critical thinking we used to spend quite a bit of time on it because it's a very common trap. We are all guilty, from time to time, of focusing on just the evidence that confirms our belief and ignoring all the evidence that refutes it.
Some examples of confirmation bias are a bit more complicated than others and people typically mix together several different fallacious forms of argument. Here's an example from Denis Alexander's book Creation or Evolution (p. 213) that combines begging the question and confirmation bias.
Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.
At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!
That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.
The post is from Dec. 1, 2015—that's only one month ago so she should be aware of all the facts concerning junk DNA.
If you are going to write about a subject in your area of expertise then it's reasonable to make yourself informed, especially if you know that the subject is controversial. For some strange reason, this common sense approach seems to be ignored when discussing genomes, evolution, and junk DNA. I don't know why some researchers think they know enough about a subject when all they've done (apparently) is read a few popular press reports.
Let's look at what Bryony Graham (@byrony_g) writes to see whether she is behaving like a proper scientist should behave when writing for the general public. It's worth noting that she was on the shortlist for the 2011 Max Perutz Science Writing Award so somebody must think she's a good science writer.
The sequence of the human genome was announced on June 26, 2000 although the actual sequence wasn't published until a year later. There were two sequences. One was the product of the International Human Genome Project led by Francis Collins who said,
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."
The sequence was a composite of a number of individuals.
The second sequence was from Celera Genomics, led by Craig Venter. It was mostly his genome, making him the second being to know his own instruction book ... right after God.
It took another seven years to finish and publish the complete sequence of all of Craig Venter's chromosomes. The paper was published in PLoS Biology (Levy et al., 2007) and highlighted in a Nature News article: All about Craig: the first 'full' genome sequence.
What's unique about this genome sequence—other than the fact that it's God's Craig Venter's—is that all 46 chromosomes were sequenced. In other words, enough data was generated to put together separate sequences of each pair of chromosomes. That produces some interesting data.
There were 4.1 million differences between homologous chromosomes (22 autosomes). 78% of these events were single nucleotide polymorphisms (SNPs). The rest were indels (insertions and deletions) and these accounted for 0.9 million nucleotides. Thus, indels made up 74% of the total number of variant nucleotide sequence.
In addition, there were 62 copy number variants (duplication) accounting for an additional 10Mb of variation between haploid sets of chromosomes. The total number of nucleotide differences is 13.9Mb when you add up all the indels, SNPs, and duplications. The two haploid genomes differ by about 0.5% by this calculation (total amount sequenced was 2,895Mb).
When the two copies of all annotated genes were compared, it turned out that 44% were heterozygous—the two copies were not identical.
Craig Venter's genome sequence differs from the composite human reference genome at 4,118,889 positions. Most of these were already known as variants in the human population but 31% were new variants (in 2007).
Venter has written about his genome sequence in A Life Decoded. He has variants in his APOE gene sequence that are associated with Alzheimer's and cardiovascular diseases. He has variants in his SORL1 that also make him at risk for Alzheimer's according to 2007 data. Just about everyone who gets their genomes sequenced will find variants that put them at greater risk for some genetic disease.
Who was Saint Valentine? Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer1 sometime around 1380. 
